open(BUFF,"./compare_affy/impute_dos") or die "no file found 1000_rsids\n";
open(WRILL,">ILL_ONLY_MARKERS");
open(WRAFF,">AFF_ONLY_MARKERS");
while(<BUFF>)
{
	chomp($_);
	@array=split(" ",$_);
	$hash{$array[0]}=1;
}
$affydir="/data4/bsi/RandD/Workflow/temp/Easy_imputer_test/GBM/AFFY";
open(AFFY_TFAM,"$affydir/fwdStrandResults_input.tped") or die "no file found $affydir/fwdStrandResults_input.tped\n";
while(<AFFY_TFAM>)
{
	chomp($_);
	@array=split(" ",$_);
	$affy{$array[1]}=1;
}
$illdir="/data4/bsi/RandD/Workflow/temp/Easy_imputer_test/GBM/ILLUMINA";
open(AFFY_TFAM,"$illdir/fwdStrandResults_input.tped") or die "no file found $illdir/fwdStrandResults_input.tped\n";
while(<AFFY_TFAM>)
{
        chomp($_);
        @array=split(" ",$_);
	$ill{$array[1]}=1;
        if(exists($hash{$array[1]}) && !exists($affy{$array[1]}))
        {
		print WRILL $array[1]."\n";
        }
}
open(AFFY_TFAM,"$affydir/fwdStrandResults_input.tped") or die "no file found $affydir/fwdStrandResults_input.tped\n";
while(<AFFY_TFAM>)
{
        chomp($_);
        @array=split(" ",$_);
	if(exists($hash{$array[1]}) && !exists($ill{$array[1]}))
	{
		print WRAFF $array[1]."\n";
	}
}

